When the CM3 came out earlier this year I immediately purchased a CMIO board (v0.3) and a CM3. I had no problem using rpiboot at the time and flashed the eMMC with the Raspbian image which was current at the time. I've finally gotten to developing the hardware the CM3 will drive so want to try and re-flash with the current stretch image but I can't mount the eMMC device?

I checked out usbboot, compiled and ran it, apparently without any problems:

I assume the CM3 still boots as it is (i.e. you're happy that the eMMC is working correctly otherwise) it's just that it doesn't appear as a MSD when the rpiboot finishes running?

Right, and that's what's confusing me. I'm not ruling out the possibility I've damaged it in some way, but it works just fine when I put it in my custom PCB or in the CMIO board with the jumper set to DIS. I have a few more modules arriving next week so hopefully I'll be able to rule that in/out.

My new batch of Compute modules arrived yesterday and they seem to be working without any problems! I've been applying the software changes I made to the first module and so far nothing has stopped rpiboot from re-mounting any of them. I don't know what I did to knacker the first one ...